2H7V

Co-crystal structure of YpkA-Rac1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	100mM HEPES pH 6.5-7.5, 5%-8% PEGMME2000 micro seeding, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.398	α = 92.08
b = 75.519	β = 103.38
c = 99.772	γ = 115.79

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 315	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2005-04-21	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2005-04-21	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1,2	2.6	95.78	99.4	0.09	11.8	3.7		51987

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.6	2.667	99.5		0.418	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 2H7O, 1MH1	2.6	95.78	51262	2552	99.39	0.224	0.222	0.222	0.257	RANDOM	62.645

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
7.3	4.77	-3.29	0.97	-0.77	-5.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.492
r_dihedral_angle_3_deg	19.171
r_dihedral_angle_4_deg	17.951
r_dihedral_angle_1_deg	7.039
r_scangle_it	2.504
r_angle_refined_deg	1.666
r_scbond_it	1.579
r_mcangle_it	1.091
r_mcbond_it	0.874
r_angle_other_deg	0.866
r_nbd_refined	0.242
r_symmetry_vdw_other	0.226
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.19
r_nbd_other	0.185
r_symmetry_hbond_refined	0.14
r_mcbond_other	0.136
r_nbtor_other	0.093
r_chiral_restr	0.084
r_xyhbond_nbd_other	0.059
r_metal_ion_refined	0.034
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7058
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing